Effect of Genetic Database Comprehensiveness on Fractional Proteomics of Escherichia coli O157:H7
Final rept. Oct 2010-Sep 2012
ARMY EDGEWOOD CHEMICAL BIOLOGICAL CENTER APG MD RESEARCH AND TECHNOLOGY DIR
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This report is required for the U.S. Army Edgewood Chemical Biological Center ECBC In-House Laboratory Independent Research project Membrane Vesicles and Extracellular Proteins in Antibiotic Resistance and Virulence. The binding of extracellular proteins membrane vesicle MV or secreted to antibiotics could contribute toward antibiotic resistance mechanisms. We are characterizing the extracellular, fimbriae, and whole cell proteins produced by the pathogenic Gram-negative bacterium Escherichia coli E. coli O157H7 in terms of proteomics and antibiotic-binding using mass spectrometry. Here we report a study on the effect of the comprehensive nature of the database used for proteomics on the analysis of various protein fractions. In this case, analysis using a more restricted database chosen based on sample knowledge resulted in identification of a higher percentage of proteins than a more comprehensive database. For E. coli O157H7, we identified proteins that were specific to certain cellular fractions. Of these, four penicillin binding proteins were identified solely in the secretome fraction. Although the three penicillin binding proteins PBPs whose functions have been determined are antibiotic targets for penicillin and they therefore do not play an antibiotic resistance role, the identification of PBPs solely in the secretome does agree with our hypothesis that antibiotic proteins would be observed in the extracellular fraction.
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